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- PDB-8evk: Crystal structure of Helicobacter pylori dihydroneopterin aldolas... -

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Basic information

Entry
Database: PDB / ID: 8evk
TitleCrystal structure of Helicobacter pylori dihydroneopterin aldolase (DHNA)
ComponentsDihydroneopterin aldolase
KeywordsLYASE / Inhibitor / Complex / Aldolase
Function / homologyDihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / dihydroneopterin aldolase activity / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / folic acid-containing compound metabolic process / PTERINE / Dihydroneopterin aldolase
Function and homology information
Biological speciesHelicobacter pylori G27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsShaw, G.X. / Cherry, S. / Tropea, J.E. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Curr Res Struct Biol / Year: 2023
Title: Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design.
Authors: Shaw, G.X. / Fan, L. / Cherry, S. / Shi, G. / Tropea, J.E. / Ji, X.
History
DepositionOct 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1793
Polymers13,9531
Non-polymers2252
Water2,414134
1
A: Dihydroneopterin aldolase
hetero molecules

A: Dihydroneopterin aldolase
hetero molecules

A: Dihydroneopterin aldolase
hetero molecules

A: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,71412
Polymers55,8134
Non-polymers9018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9720 Å2
ΔGint10 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.081, 68.081, 57.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-384-

HOH

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Components

#1: Protein Dihydroneopterin aldolase


Mass: 13953.307 Da / Num. of mol.: 1 / Fragment: Full-length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Strain: G27 / Gene: HPG27_1434 / Plasmid: pJT250 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: B5Z9C8
#2: Chemical ChemComp-PE0 / PTERINE


Mass: 163.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.24 % / Mosaicity: 1.601 ° / Mosaicity esd: 0.012 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: (NH4)2SO4, NaCl, etc.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2013 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→30 Å / Num. obs: 21197 / % possible obs: 98.2 % / Redundancy: 14.1 % / Biso Wilson estimate: 22.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.036 / Rrim(I) all: 0.136 / Χ2: 0.96 / Net I/av σ(I): 17.45 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allΧ2% possible all
1.49-1.549.41.1917690.5470.8410.6520.82282.6
1.54-1.6112.92.3321710.7720.9340.4140.918100
1.61-1.6814.13.6121090.8730.9660.2760.951100
1.68-1.7714.45.3921640.940.9840.1780.994100
1.77-1.8814.78.5221490.9890.9970.1030.99100
1.88-2.0214.913.1121600.9890.9970.0590.986100
2.02-2.2315.115.8121570.9920.9980.0440.97100
2.23-2.5515.217.5321650.9920.9980.0380.992100
2.55-3.2115.117.8121610.9940.9980.0340.967100
3.21-3014.820.0421920.9930.9980.0280.93999.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O90

2o90


Resolution: 1.49→26.9 Å / SU ML: 0.2427 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1004 4.74 %Random selection
Rwork0.1974 20165 --
obs0.199 21169 98.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.63 Å2
Refinement stepCycle: LAST / Resolution: 1.49→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 16 134 1097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811101
X-RAY DIFFRACTIONf_angle_d0.99051491
X-RAY DIFFRACTIONf_chiral_restr0.0816170
X-RAY DIFFRACTIONf_plane_restr0.0062186
X-RAY DIFFRACTIONf_dihedral_angle_d14.6578439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.570.44611280.38352639X-RAY DIFFRACTION90.54
1.57-1.670.30261420.28382896X-RAY DIFFRACTION99.97
1.67-1.80.28971440.26092926X-RAY DIFFRACTION99.97
1.8-1.980.27071440.24372897X-RAY DIFFRACTION99.97
1.98-2.260.25721460.21342926X-RAY DIFFRACTION100
2.26-2.850.24691510.20722928X-RAY DIFFRACTION100
2.85-26.90.18521490.15592953X-RAY DIFFRACTION99.58

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